I'm working on a custom board based on the XU224. I have been flashing/running programs happily from xtime composer with the xtag3 programmer what must have been hundreds of times when suddenly (without changing any hardware or code) I can no longer do either and I get this error:

And no other feedback. Interestingly the board boots and runs fine on the code which is on the flash chip from before I lost the ability to program the thing.

When I make an attempt, the existing code on the board stops executing, the processor appears to reset and the xtag 3 LEDS will go on (5 blinking or steady green plus one red LED). That continues until something times out in about 20/30 seconds and I get the above error message.

As to using XRUN, I assume you mean over USB and this board doesn't have a separate USB port unfortunately. It's the XTAG port or bust and I can't really let it be bust. The Xtime IDE still detects the target via the xtag but then can't do anything except for resetting the board. It's got me a bit baffled as if it can detect the target and reset the board that would imply that the debug port on the xmos chip is at least mostly working (and there isn't exactly much to go wrong there). The fact that the chip will happily boot and run off whats on the flash implies that all the boot, power cycling and tile 2 set up pull ups are working which leaves...?

From the command line, I assume xrun -l completes OK? This queries the JTAG modules on each node.

The loading process is quite complex behind the scene. Yes there is the communication with the JTAG module but If either one of the processors can't run properly (reset, power good, decoupling, clock etc.) then it can prevent loading and give you a message as seen (it first loads a bootloader before the actual binary). Have you made any changes to the HW or even the xn file recently?